27 December 2010

The New Mild Multi-Regionalism

The first, based on a comparison of a total Neanderthal genome recovered from ancient remains to modern humans suggests that non-Africans have an average of 1% to 4% Neanderthal admixture distributed more or less evenly across the non-African world, relative to Africans. Multiple mtDNA samples from Neanderthals show that no modern human has any Neanderthal mtDNA, and there are strong, although less direct, reasons to suspect that there is likely no non-recombining Neanderthal Y-DNA in modern humans. As I've mentioned previously, this is surprising, as modern humans outside the Neanderthal range have the same level of Neanderthal admixture as those within the Nenaderthal range, suggesting that the admixture that survives in today's modern humans at detectable levels derives largely from admixture with a Eurasian founder population (or alternatively, from population structure in Africa in which the source population for Eurasians was more similar genetically to Neanderthals and has since largely vanished from genetically well sampled populations of Africa).

Papuans Have Denisovian Ancestors

The second, based on comparison of a total genome recovered from remains in the Denisova cave in South Siberia from 49,000 years ago (a population dubbed the Denisovians for now, in order to maintain agnosticism as to their species association within the Homo genus) to modern humans suggests that about 5% of the DNA in Melanesian populations (i.e. New Guinea) relative to Africans are derived from the Denisovians, and that there are smaller levels of Denisovian ancestry in other modern human populations. The two samples of mtDNA from the Denisovians are unlike both Neanderthal and modern human mtDNA, and a Densivoian contribution to modern human non-recombining Y-DNA is unlikely for the same reasons that it is unlikely in the case of Neanderthals. The autosomal DNA of the Denisovians show them to be more similar to Neanderthals than to modern humans, although still very different from both.

Since Melanesians are also non-Africans, it appears that as much as 7.25% of Melanesian autosomal DNA may be derived from archiac humans (i.e. Neanderthals and Denisovians combined), about one-fourteenth of their ancestry, which is more than one grandparent of a grandparent (although it isn't so recent or so direct, and instead likely reflects a small nubmer of admixture events with small founder populations, possibly over an extended period of time of co-existence of archaic Homo populations with modern humans).

The immense geographic distance from New Guinea, where Denisovian genetic traces are found, to Southern Siberia where the Denisovian DNA was found, also suggests that the Denisovian range may have once stretched as far as Southeast Asia, with admixture with proto-Melanesians taking place perhaps in Sahul.

The Denisovian remains are found in association with what seems like Mousterian artifacts typical of Neanderthal sites, rather than the earlier, more simple artifacts typically associated with Homo Erectus sites.

Early Warnings

Two other recent discoveries, while not from 2010, add to the stew.

First, there is Homo floresiensis (colloquially called Hobbits), a cluster of skeletons of apparently archaic humans remains from about 20,000 years ago (although the dating and taxonomy are disputed) whose discovery on the island of Flores was announced in 2004, that may have co-existed with modern humans and even survived to be mentioned in modern human folklore from the island. Some scholars have argued that they were simply modern humans with some sort of disorder, but the better supported view seems to be that they were a population archaic humans, perhaps a relict population of Homo Erectus, or if they were distinct from Homo Erectus, the Denisovians.

Also, while no one disputes the Cro-Magnons in Europe were anatomically modern humans descended from the same Out of Africa founder population as all modern humans living today, there is incresing evidence that Cro-Magnons were racially very distinct from subsequent Europeans -- as visibly and genetically different from Neolithic farmers as Australian Aborigines are from the people of Europe today.

The extent to which the people of Europe today trace their ancestry to Cro-Magnons is disputed. There has been a little bit of influx of Asian ancestry from Siberia that can be detected in the genetics of Uralic language speaking populations such as the Finns and the Estonians. There has been a substantial population influx to Europe from the Near East and by West Eurasian peoples from Central Asia and/or the Caucuses in the last 20,000 years, although the mix of ancestry varies from region to region in Europe. But, opinion differs on a Cro-Magnon contribution (although all serious commentators agree that it might vary from one part of Europe to another). Some argue for a negligible contribution, while others argue for as much as an 80% contribution in some parts of Europe.

The Not So Old Consensus Worldview

Two years ago, the overwhelming consensus among scholars in the evolution of modern humans, mostly anthropologist and geneticists, had been that there was no, or virtually no archaic Homo ancestry in modern humans. If Neanderthal or Homo Erectus had sex or had children, their offspring did not survive to the present.

Instead, the consensus view held, all modern humans are descendants from an African Mitochondrial Eve and Y-DNA Adam, and that virtually all non-Africans descend from a founder population that was a subset of all Africans, with two separate non-African mtDNA lineages tracing their roots to the most basal mtDNA L3 lineage in Africa, and all non-African Y-DNA lineages tracing their roots to two African rooted Y-DNA lineages, CF and DE. The remaining mtDNA L lineages, and the Y-DNA A and B lineages, in contrast, are seen as native to Africa and as never having been a part of the Out of Africa founder population (although some African lineage members have since left the continent, mostly to adjacent parts of Europe and the Near East, or in migrations documented or strongly suggested to be from in the historic era).

A currently small minority view imagines that a common ancestor of Y-DNA lineages CF and DE was Eurasian and that Y-DNA lineage E, which is now predominant in sub-Saharan African and virtually absent except in areas immediately adjacent to Africa or in places where there was historic era migration, was a back migration to Africa. In my view, the evidence more strongly favors a scenario where the main Out of Africa population derives from Y-DNA lineage CF, and Y-DNA lineage D found in West Africa, the Andaman Islands, Tibet, Japan, and Siberia, was an early and separate wave of Out of Africa migration paired with some of the early mtDNA M lineages.

The timing of the Out of Africa migration or migrations is a matter of ongoing controversy. At least some of the Out of Africa migrations had to have taken place by 50,000 years ago, based on the presence of the archaeologically documented anatomically modern humans (and ancient mtDNA of modern Eurasian lineages) in Europe, Papua New Guinea and Australia starting around 50,000 years ago. The oldest evidence of arguably modern human traces outside Africa go back as far as perhaps 120,000 years ago. There are anatomically modern human remains that old in the Levant, although it appears that this modern human presence outside of Africa was interrupted for tens of thousands of years before being re-established, and there are anatomically modern human remains in India that appear to be from about 75,000 years ago. There a very small number of Homo remains (whose taxonomy and dating are disputed) in China as old as 100,000 years ago or so. The multi-regionalist claim that modern humans evolved in multiple places that reflect different modern races was essentially routed, with all serious scholars agreeing that modern humans evolved in Africa perhaps 200,000 years ago, or perhaps a bit earlier, from archaic Homo types most closely related to Neanderthals who split off from their common ancestor with modern humans perhaps 500,000 years ago.

New fossil finds could always push back the oldest Out of Africa date, of course, but no one really expects to find modern humans outside Africa more than 200,000 years ago before the earliest modern human remains in Africa.

The Neanderthal record, to the exclusion of modern humans, is fairly continuous in Europe until around 30,000 years ago when they went extinct after tens of thousands of years of co-existence with modern humans in Europe and the Near East (interrupted at some points). Up through around 200,000 years ago, there is also a fossil record of archaic humans in Asia, which tended to be lumped together as Homo Erectus, although not without splitters who urged finer distinctions.

In the old worldview, all of the archaic Homo populations Eurasia were dead ends that left no genetic trace in modern humans anywhere, and their differences from modern humans were emphasized.

Even many of the early anatomically modern human populations have been reduced to insignificance with only faint genetic traces by subsequent migrating populations that were more successful and either wiped out or overwhelmed from a population genetic perspective, their predecessors.

The New Worldview

The ancient DNA evidence from Neanderthals and the Denisovians has shaken up the consensus. Archaic Homo types have made their way into the post-Out of Africa, post-evolution of anatomically modern humans, modern human family tree as a significant, but minor part of the total genome of part, but not all, of the human race.

While the vast majority of our ancestry is shared by all modern humans, a little of the ancestry of some modern humans in archaic. Not all modern humans share a common set of ancestors until one looks back as far as the common ancestor of Neanderthals and modern humans (or perhaps even further). The line between species, subspecies and race is beginning to look more arbitrary, and the fact that there were hybrid archaic and modern humans forces us to rethink who archaic modern humans were in relation to us.

There are a lot of open questions.

The mutation clock evidence from the Denisovian autosomal DNA on the timeline of the events that gave rise to their admixture with modern humans makes no sense, and is also a poor fit to the mtDNA mutation clock evidence.

It isn't clear which Homo remains and Paleolithic industries, if any outside of Denisovia yet found, should be associated with the Denisovians. Were they another race of Neanderthals? Homo Erectus? A hybrid Homo Erectus and Neanderthal population? A hybrid modern human and Neanderthal population? A hybrid Homo Erectus and modern human population? Were they Homo floresiensis? Were they something else entirely?

Are there other cases of archaic admixture yet to be discovered? How many archaic Homo types were there? Where there stable hybrid populations that were distinct from the pure types?

Where did the admixtures with archaic Homo take place? Was it bidirectional? How did it happen?

Why do we have autosomal traces of archaic Homo but not mtDNA and Y-DNA traces? What does that imply about the extent to which archaic Homo were separate species from modern humans?

In what ways does our archaic Homo ancestry make those of us who have it different? Does it include adapative traits? Does it include non-adaptive traits? Is it irrelevant except to the extent that it is ancestry identifying?

Should we reinterpret transitional period fossils to reflect our new understanding of the mix of Homo types that were present in the Paleolithic?

Were there archaic types with whom modern humans after their initial evolution admixed in Africa as well, and if so, are their some African lineages that show a stronger affinity to those archaic Homo types than others? Which archaic Homo types admixed with modern humans?

And, the old questions haven't gone away either. How many major demographic waves of human migration where there in pre-history, and when and where did they happen? Which waves admixed with modern archaic humans and which did not? From which demographic waves do today's modern human populations derive? Why did each of the archaic human populations cease to exist as distinct populations? When did the last pureblooded archaic human die? What did we take culturally from archaic humans and how? How did archaic humans differ from modern humans? Were those differences the cause of modern human survival, or did modern humans triumph largely as a matter of luck?

When did the various language families spoken today or known to have died come into being, and how did they spread and grow distinct? What is the oldest knowable linguistic stata in pre-history that we can say anything about and what do we know about what it was like and when and where it prevailed? When was language shift due to population replacement and when was it due to culturally transition? How did the cultural transitions happen? How closely are modern political, linguistic and ethnic divides linked to particular genetically distinct populations? How long does the cultural legacy of pre-historic events influence people in the present? Do our genetic roots matter? To what extent are modern humans the product of genetic and/or epigenetic adaptations to material circumstances that no longer exist? How fast are we evolving now, and in what respects and why?